Scientific Visualization

Transcription

1 Scientific Visualization Lecture 7: Other Visualization software Patrik Malm Centre for Image Analysis Swedish University of Agricultural Sciences Uppsala University

2 Today's lecture Ways to create visualizations using Matlab Blender

3 Opposite ends of the scale Matlab Scientific tool Good for visualizing distributions of data Expensive Blender Open source 3D-modeling software Free Harder (but NOT impossible) to do exact scientific visualizations

4 Matlab Developed by The MathWorks First appeared in the late 1970s Short for Matrix Laboratory All variables are matrices Several modules, e.g., Image processing toolbox Cross-platform Can be slow or fast depending on application type

5 Matlab Visualizations Plot options And many, many more...

6 Matlab Visualizations Available plot-types depend on which toolboxes are installed. Huge amount of user written functions at Mathwork file exchange Easy to modify and/or create own visualization functions

7 Matlab Import and Export Import and export of 'special' data very much dependent on user scripts Example: writevtk.m

8 Matlab Import and Export

9 Matlab - Links

10 Blender Free 3D modeling and animation software Features include Physics and Particles Liquid and softbody simulations Game creation Python support for scripting Video sequencer Available for all common OS (installation file sized around Mb)

11 Blender History Initially developed as an in-house application by the Dutch animation studio NeoGeo and Not a Number Technologies (NaN) during the late 90's NaN bankrupt 2002 (Blender v 2.25) Released under the GNU GPL for a one time payment of 100,000 Euros Blender is now managed by the Blender Foundation Version 2.5 is soon to be released

12 Blender Strengths: Free (!!!) Powerful Interface for python scripting Large user community -> tons of online material Weaknesses: Confusing user interface (Under major reconstruction) Sometimes hard to find good documentation

13 Blender User interface

14 Blender Getting around 'Middle mouse button' (MMB) Rotate view 'Shift' + 'MMB' Pan view 'Scroll wheel' Zoom 'Ctrl' + 'MMB' Zoom 'Numpad 1, 3, 7' Front, right and top view 'Left mouse button' (LMB) Move 3D cursor

15 Blender Object selection Right mouse button (RMB) Selects objects 'Shift' + RMB Select multiple objects, deselect objects 'A' Select all, clear selection 'B' Box select 'B' + 'B' Brush select (edit mode only)

16 Blender Edit mode vs. Object mode 'TAB' key used to switch between modes for selected object In 'Object mode' the user can perform actions that affect the entire object (translation, scale, rotation,...) In 'Edit mode' local changes can be made by manipulating the vertices that the object consists of

17 Blender Object manipulation 'G' Grab (Move objects) 'R' Rotate 'S' Scale 'X' Delete 'E' Extrude (Edit mode) 'Z' Shaded/Unshaded view 'Shift' + 'D' Duplicate 'Ctrl' + 'Z' Undo Golden Rule Always keep one hand on the keyboard!

18 Blender Rendering Numpad '0' Shows the camera view 'F12' renders using current settings and camera, light positions Internal renderer supports ray-tracing Several external rendering engines supported (Yafray, Indigo) It is possible to make image composition (effects) in Blender based on the render layers

19 Blender Loading and saving Save & Load.blend files 'Ctrl' + 'w' Open save file dialog 'Ctrl' + 'o' Open recent 'F1' Open load file dialog Save render result 'F3' Open save image dialog

20 Blender Object structure

21 Blender Object structure Structure of a file can be seen using the OOPSschematic view OOPS-schematic for a small scene

22 Blender Node composition Built-in post-processing of your render

23 Blender Node composition Effect of the 'Glare'-node

24 Blender Node composition Possible to separate and manipulate different layers of the render result

25 Blender Sequence editor A very powerful tool for editing movies Can combine multiple video clips, sound and add effects to create a final result Can be used together with node editor to add more control

26 Blender Sequence editor

27 Blender Import and Export Import/Export scripts exist for several common 3Dformats Open source quality Writing custom scripts possible

28 Blender Python scripting Blender has its own Python API Possible to control most of the functionality through Python scripts Learning threshold determined by ability to pick up Python

29 Blender Python scripting 'Alt' + 'p' to run

30 Blender Import example # Import Demo import Blender from Blender import * import bpy import math from math import * f=open("/home/patrik/pythondata.dat") coords=[] edges=[] counter = 0 for l in f: l=l.split(',') d=[float(l[0]),float(l[1]),float(l[2])] coords.append(d) counter = counter + 1 print(counter) if counter > 1: edges.append([counter 2,counter 1]) me = Mesh.Primitives.UVsphere(6,6,0.2) # create a primitive sc = Scene.GetCurrent() ob2 = sc.objects.new(me) ob2.setlocation(d) # get current scene # add a new mesh type object to the scene me = bpy.data.meshes.new() me.verts.extend(coords) me.edges.extend(edges) scn = bpy.data.scenes.active ob = scn.objects.new(me) # create empty mesh # populate with vertices # create edges # link object to current scene Blender.Redraw()

31 Blender Import example

32 Blender SCIENTIFIC visualizations Blender is used at scientific groups over the world Free and open source but still powerful the main selling points Uses include Electron microscope data visualizations ( Population behavior simulation using the Blender game engine ( Molecular visualization and simulation (

33 Blender Some links A few links that could be interesting (Gävle högskola summer course)